Typical raw products of high alpha Fischer-Tropsch hydrocarbon synthesis (FT-HCS) are too heavy and too waxy for use as diesel fuel. Therefore, FT-HCS products are universally hydroprocessed to simultaneously reduce the boiling point and improve cold flow properties. In addition hydroprocessing removes any oxygenates and olefins produced during FT-HCS, by converting them to the corresponding paraffins. The removal of olefins and oxygenates is desirable because high olefin contents are directly related to poor oxidative stability and carboxylic acids result in fuel corrosivity. But the complete removal oxygenates including high molecular weight linear primary alcohols is undesirable in that Fischer-Tropsch distillates that retain native long chain primary alcohols exhibit surprisingly high lubricity. Prior art processes maximize the desirable oxygenates, while minimizing undesirable carboxylic acids, and olefins. All of these flow plans require a degree of over hydroprocessing in order to assure product compositions within the desired range. This over processing results in undesirable increases in capital costs and higher operational costs from larger recycle streams and hydrogen consumptions. The ability to control secondary hydroprocessing would therefore allow the continual optimization of the operations, while minimizing both capital and operational expenses. The present invention provides for the use of infra-red spectroscopy to provide real time operational control of a novel flow scheme to produce a high lubricity, high stability Fischer-Tropsch derived diesel fuels and blend stocks. Infrared spectroscopy allows for rapid and reproducible measurement of key olefin, alcohol, and carboxylic acid concentrations in both process streams and final products.